The Spurs, who have one of the oldest rosters in the league, sent four of their top players home to rest before Thursday's game, which was the final game of a six-game road trip for San Antonio and their fourth game in five nights.
"The Spurs decided to make four of their top players unavailable for an early-season game that was the team's only regular-season visit to Miami," NBA Commissioner David Stern said.
"The team also did this without informing the Heat, the media, or the league office in a timely way. Under these circumstances, I have concluded that the Spurs did a disservice to the league and our fans."
Spurs head coach Gregg Popovich decided to send Tim Duncan, Tony Parker, Manu Ginobili and Danny Green home rather than inserting them into the line-up against the defending NBA champion Heat.
Despite missing the top players, the Spurs nearly shocked the Heat, leading 98-93 with about two minutes to play, before Miami's big guns led the team to a 105-100 victory.
The fine was not a surprise as Stern sent out a statement late on Thursday apologising to NBA fans for Popovich's decision and promising "substantial sanctions”.
San Antonio's next game is at home on Saturday against the Memphis Grizzlies.